Mass spectrometry allows the determination of the mass-to-charge ratio (m/z) of ions of sample molecules. Mass spectrometry involves ionizing the sample molecule or molecules and then analyzing the ions in an analyzer that has a detector. Various mass spectrometers are known.
Tandem mass spectrometry involves ionization of a sample into ions, which are introduced into a mass analyzer. The mass analyzer selects parent ions of a desired m/z for further analysis. The parent ions are then fragmented by one or more of a variety of methods into product ions. The product ions are then analyzed by a mass analyzer to determine the mass-to-charge ratios of the product ions and thus obtain a mass spectrum of the product ions. Tandem mass spectrometry has become increasingly important for the analysis of bio-molecules such as peptides and proteins, and enables the determination of amino acid sequence of peptides and proteins.
Fragmentation of parent ions is typically accomplished using collision-induced dissociation (CID), which involves colliding the parent ions with gas atoms or molecules in order to fragment the parent ions. Other methods of fragmenting parent ions are known, such as, for example, electron capture dissociation (ECD). Electron capture dissociation involves the capture of low energy electrons by ions, which leads to the subsequent fragmentation of the ions. Electron capture dissociation produces cleavage patterns of polypeptides that are different than cleavage patterns of polypeptides produced by CID, and the nature of the cleavage patterns makes ECD a desirable fragmentation method for analysis of peptides and proteins by tandem mass spectrometry (see, e.g., Kruger et al., Electron capture dissociation of multiply charged peptide cations, International Journal of Mass Spectrometry, 185–187, 787–793 (1999); Kruger et al., Electron capture versus energetic dissociation of protein ions, International Journal of Mass Spectrometry, 182–183, 1–5 (1999); Zubarev et al., Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process, J. Am. Chem. Soc., 120, 3265–3266 (1998); and Zubarev et al., Electron Capture Dissociation for Structural Characterization of Multiply Charged Protein Cations, Anal. Chem., 72, 563–573 (2000)).
Electron capture dissociation is typically performed using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Electron capture dissociation is performed in such an instrument by trapping parent ions in the FT-ICR cell and reacting the trapped ions with electrons that are injected into the cell. The product ions that result are also mass analyzed using the FT-ICR cell. Although analysis of peptides and proteins by tandem mass spectrometry using ECD for fragmentation is desirable, the use of ECD has been limited due to both the large size and the expense of FT-ICR mass spectrometers.